Addressed failing tests

refactored tests

analyses/models.py

@@ -27,6 +27,7 @@
 from analyses.base_models.with_downloads_models import WithDownloadsModel
 from emgapiv2.async_utils import anysync_property
 
+
 # Some models associated with MGnify Analyses (MGYS, MGYA etc).
 
 
@@ -84,14 +85,6 @@ def private_only(self):
         return self.get_queryset(private_only=True)
 
 
-class PublicStudyManager(BasePublicStudyManager, models.Manager):
-    """
-    A custom manager that filters out private studies by default.
-    """
-
-    pass
-
-
 class StudyManager(models.Manager):
     async def get_or_create_for_ena_study(self, ena_study_accession):
         logging.info(f"Will get/create MGnify study for {ena_study_accession}")
@@ -113,6 +106,13 @@ async def get_or_create_for_ena_study(self, ena_study_accession):
         )
         return study
 
+class PublicStudyManager(BasePublicStudyManager,  StudyManager):
+    """
+    A custom manager that filters out private studies by default.
+    """
+
+    pass
+
 
 class Study(MGnifyAutomatedModel, ENADerivedModel, TimeStampedModel):
     objects = PublicStudyManager()

analyses/tests.py

@@ -3,19 +3,27 @@
 import tempfile
 
 import pytest
+from django.contrib.auth.models import User
 from django.core.management import call_command
+from django.urls import reverse
+from rest_framework import status
 
 from ena.models import Study as ENAStudy
-
+from .management.commands.import_v5_analysis import logger
 from .models import (
     Analysis,
     Assembler,
-    Assembly,
     Biome,
     ComputeResourceHeuristic,
     Run,
-    Study,
-)
+    Study, )
+
+def create_analysis(is_private=False):
+    run = Run.objects.first()
+    return Analysis.objects.create(
+        study=run.study, run=run, ena_study=run.ena_study, sample=run.sample,
+        is_private=is_private
+    )
 
 
 @pytest.mark.django_db(transaction=True, reset_sequences=True)
@@ -30,12 +38,12 @@ def test_biome_lineage_path_generator():
     assert Biome.lineage_to_path("root") == "root"
     assert Biome.lineage_to_path("Root") == "root"
     assert (
-        Biome.lineage_to_path("root:Host-associated:Human:Digestive system")
-        == "root.host_associated.human.digestive_system"
+            Biome.lineage_to_path("root:Host-associated:Human:Digestive system")
+            == "root.host_associated.human.digestive_system"
     )
     assert (
-        Biome.lineage_to_path("root:Host-associated:Human:Digestive system (bowel)")
-        == "root.host_associated.human.digestive_system_bowel"
+            Biome.lineage_to_path("root:Host-associated:Human:Digestive system (bowel)")
+            == "root.host_associated.human.digestive_system_bowel"
     )
 
 
@@ -186,7 +194,7 @@ def test_biome_importer(httpx_mock):
 
 @pytest.mark.django_db(transaction=True)
 def test_analysis_inheritance(
-    raw_read_run,
+        raw_read_run,
 ):
     for run in Run.objects.all():
         analysis = Analysis.objects.create(
@@ -196,3 +204,125 @@ def test_analysis_inheritance(
         analysis.refresh_from_db()
         assert analysis.experiment_type != analysis.ExperimentTypes.UNKNOWN
         assert analysis.experiment_type == run.experiment_type
+
+
+########## PRIVACY TESTS##########
+########## PRIVACY TESTS ##########
+
+#
+# @pytest.mark.django_db(transaction=True)
+# def test_public_api_studies_endpoint(api_client):
+#     """Test that public API only returns public studies"""
+#     public_study = Study.objects.create(title="Public Study", is_private=False)
+#     private_study = Study.objects.create(title="Private Study", is_private=True)
+#
+#     url = reverse("api:list_mgnify_studies")
+#     response = api_client.get(url)
+#
+#     assert response.status_code == status.HTTP_200_OK
+#     assert len(response.json()['items']) == 1  # Only public study
+#     # log response.json()
+#     # logger.info('RESPONSE JSON   ')
+#     # logger.info(response.json())
+#
+#     assert response.json()["items"][0]["accession"] == public_study.accession
+#
+#
+# @pytest.mark.django_db(transaction=True)
+# def test_public_api_analyses_endpoint(raw_read_run, api_client):
+#     """Test that public API only returns public analyses"""
+#     public_analysis = create_analysis(is_private=False)
+#     create_analysis(is_private=True)
+#
+#     url = reverse("api:list_mgnify_analyses")
+#     response = api_client.get(url)
+#
+#     assert response.status_code == status.HTTP_200_OK
+#     # Only public analysis should be returned
+#     assert len(response.json()['items']) == 1
+#     assert response.json()['items'][0]["accession"] == public_analysis.accession
+#
+#
+# @pytest.mark.django_db(transaction=True)
+# def test_admin_view_studies(admin_client):
+#     """Test that admin interface shows all studies"""
+#     public_study = Study.objects.create(title="Public Study", is_private=False)
+#     private_study = Study.objects.create(title="Private Study", is_private=True)
+#
+#     url = reverse("admin:analyses_study_changelist")
+#     response = admin_client.get(url)
+#
+#     assert response.status_code == 200
+#     content = response.content.decode("utf-8")
+#     assert public_study.title in content
+#     assert private_study.title in content
+#
+#
+# @pytest.mark.django_db(transaction=True)
+# def test_admin_view_analyses(raw_read_run, admin_client):
+#     """Test that admin interface shows all analyses"""
+#     public_analysis = create_analysis(is_private=False)
+#     private_analysis = create_analysis(is_private=True)
+#
+#     url = reverse("admin:analyses_analysis_changelist")
+#     response = admin_client.get(url)
+#
+#     assert response.status_code == 200
+#     content = response.content.decode("utf-8")
+#     assert public_analysis.accession in content
+#     assert private_analysis.accession in content
+#
+#
+# @pytest.mark.django_db(transaction=True)
+# def test_study_manager_methods():
+# # def test_manager_methods(raw_read_run):
+#     """Test various manager methods for privacy handling"""
+#     ena_study = ENAStudy.objects.create(accession="PRJ1", title="Project 1")
+#     public_study = Study.objects.create(ena_study=ena_study, title="Public Study", is_private=False)
+#     private_study = Study.objects.create(title="Private Study", is_private=True)
+#
+#     assert Study.objects.count() == 1
+#     assert Study.objects.first() == public_study
+#     assert Study.all_objects.count() == 2
+#     private_studies = Study.objects.private_only()
+#     assert private_studies.count() == 1
+#     assert private_studies.first() == private_study
+#
+# @pytest.mark.django_db(transaction=True)
+# def test_manager_analysis_methods(raw_read_run):
+#     public_analysis = create_analysis(is_private=False)
+#     private_analysis = create_analysis(is_private=True)
+#
+#     assert Analysis.objects.count() == 1
+#     assert Analysis.objects.first() == public_analysis
+#     assert Analysis.all_objects.count() == 2
+#     private_analyses = Analysis.objects.private_only()
+#     assert private_analyses.count() == 1
+#     assert private_analyses.first() == private_analysis
+#
+#     public_analysis.annotations = {"test": "data"}
+#     public_analysis.save()
+#
+#     analysis = Analysis.objects_and_annotations.first()
+#     assert analysis.annotations == {"test": "data"}
+#     all_analyses = Analysis.all_objects_and_annotations.all()
+#     assert len(all_analyses) == 2
+#
+#
+# @pytest.fixture
+# def api_client():
+#     from rest_framework.test import APIClient
+#
+#     return APIClient()
+#
+#
+# @pytest.fixture
+# def admin_client():
+#     from django.test import Client
+#
+#     admin_user = User.objects.create_superuser(
+#         username="admin", email="[email protected]", password="adminpass123"
+#     )
+#     client = Client()
+#     client.force_login(admin_user)
+#     return client

emgapiv2/test_data_privacy.py

@@ -0,0 +1,133 @@
+import pytest
+from django.contrib.auth.models import User
+from django.core.management import call_command
+from django.urls import reverse
+from rest_framework import status
+
+from analyses.management.commands.import_v5_analysis import logger
+from analyses.models import Run, Analysis, Study
+from ena.models import Study as ENAStudy
+
+
+def create_analysis(is_private=False):
+    run = Run.objects.first()
+    return Analysis.objects.create(
+        study=run.study, run=run, ena_study=run.ena_study, sample=run.sample,
+        is_private=is_private
+    )
+
+@pytest.mark.django_db(transaction=True)
+def test_public_api_studies_endpoint(api_client):
+    """Test that public API only returns public studies"""
+    public_study = Study.objects.create(title="Public Study", is_private=False)
+    Study.objects.create(title="Private Study", is_private=True)
+
+    logger.info("Public study SURFACE  BEING TESTED IN NEW SEPARATE TEST FILE")
+
+    url = reverse("api:list_mgnify_studies")
+    response = api_client.get(url)
+
+    assert response.status_code == status.HTTP_200_OK
+    assert len(response.json()['items']) == 1  # Only public study
+
+    assert response.json()["items"][0]["accession"] == public_study.accession
+
+
+@pytest.mark.django_db(transaction=True)
+def test_public_api_analyses_endpoint(raw_read_run, api_client):
+    """Test that public API only returns public analyses"""
+    public_analysis = create_analysis(is_private=False)
+    create_analysis(is_private=True)
+
+    url = reverse("api:list_mgnify_analyses")
+    response = api_client.get(url)
+
+    assert response.status_code == status.HTTP_200_OK
+    # Only public analysis should be returned
+    assert len(response.json()['items']) == 1
+    assert response.json()['items'][0]["accession"] == public_analysis.accession
+
+
+@pytest.mark.django_db(transaction=True)
+def test_admin_view_studies(admin_client):
+    """Test that admin interface shows all studies"""
+    public_study = Study.objects.create(title="Public Study", is_private=False)
+    private_study = Study.objects.create(title="Private Study", is_private=True)
+
+    url = reverse("admin:analyses_study_changelist")
+    response = admin_client.get(url)
+
+    assert response.status_code == 200
+    content = response.content.decode("utf-8")
+    assert public_study.title in content
+    assert private_study.title in content
+
+
+@pytest.mark.django_db(transaction=True)
+def test_admin_view_analyses(raw_read_run, admin_client):
+    """Test that admin interface shows all analyses"""
+    public_analysis = create_analysis(is_private=False)
+    private_analysis = create_analysis(is_private=True)
+
+    url = reverse("admin:analyses_analysis_changelist")
+    response = admin_client.get(url)
+
+    assert response.status_code == 200
+    content = response.content.decode("utf-8")
+    assert public_analysis.accession in content
+    assert private_analysis.accession in content
+
+
+@pytest.mark.django_db(transaction=True)
+def test_study_manager_methods():
+# def test_manager_methods(raw_read_run):
+    """Test various manager methods for privacy handling"""
+    ena_study = ENAStudy.objects.create(accession="PRJ1", title="Project 1")
+    public_study = Study.objects.create(ena_study=ena_study, title="Public Study", is_private=False)
+    private_study = Study.objects.create(title="Private Study", is_private=True)
+
+    assert Study.objects.count() == 1
+    assert Study.objects.first() == public_study
+    assert Study.all_objects.count() == 2
+    private_studies = Study.objects.private_only()
+    assert private_studies.count() == 1
+    assert private_studies.first() == private_study
+
+@pytest.mark.django_db(transaction=True)
+def test_manager_analysis_methods(raw_read_run):
+    public_analysis = create_analysis(is_private=False)
+    private_analysis = create_analysis(is_private=True)
+
+    assert Analysis.objects.count() == 1
+    assert Analysis.objects.first() == public_analysis
+    assert Analysis.all_objects.count() == 2
+    private_analyses = Analysis.objects.private_only()
+    assert private_analyses.count() == 1
+    assert private_analyses.first() == private_analysis
+
+    public_analysis.annotations = {"test": "data"}
+    public_analysis.save()
+
+    analysis = Analysis.objects_and_annotations.first()
+    assert analysis.annotations == {"test": "data"}
+    all_analyses = Analysis.all_objects_and_annotations.all()
+    assert len(all_analyses) == 2
+
+
+@pytest.fixture
+def api_client():
+    from rest_framework.test import APIClient
+
+    return APIClient()
+
+
+@pytest.fixture
+def admin_client():
+    from django.test import Client
+
+    admin_user = User.objects.create_superuser(
+        username="admin", email="[email protected]", password="adminpass123"
+    )
+    client = Client()
+    client.force_login(admin_user)
+    return client